[gmx-users] the temperature effect in the simulation

[He, Yang]

Hi Justin,

My box size is 3.13690   3.73000   2.70000 and I  use  the user-defined potential functions.

#define _FF_GROMACS
#define _FF_GROMACS1

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  1                     1               no                  1.0       1.0

#include "ffyxhnb.itp"
#include "ffyxhbon.itp"

This is my ffyxh.itp file

Also  I have change the value of  tau_t by 0.1 but it did not work.

Please let me know if you need any further information.

Thank you.

Yang
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Tuesday, November 11, 2008 12:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the temperature effect in the simulation

He, Yang wrote:
> Hi all users,
>
> When I change the temperature to try to get different disassociation about the two DNA's strands. But even I change the value of temperature by 0K in the mdp file ,
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl                   = berendsen
> ; Groups to couple separately
> tc-grps                  = System
> ; Time constant (ps) and reference temperature (K)
> tau_t                    = 0.001
> ref_t                    = 300

I don't know if this is relevant or not, but a coupling constant of 0.001 is
exceptionally short.  What is the timestep in your simulation?  Typically one
sees tau_t = 0.1 with a timestep of 0.001-0.002 ps.

> ; Pressure coupling
> Pcoupl                   = no
> Pcoupltype               = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau_p                    = 0.5
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> ; Random seed for Andersen thermostat
> andersen_seed            = 815131
>
> It  will also disassociate .It is strange.

So the dissociation occurs at 0K and 300K?  Sounds like something is
fundamentally flawed with your system setup.  How large is your box?  What force
field are you using?

-Justin

>
> Can anyone of you tell me what is the reason for that?
>
> Thank you in advance.
>
> Yang
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--
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
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